OSX Apache using wrong version of PHP

Did you follow all the instructions provided in the Caveats?

Run brew info php54 to see them again.

Especially the line:

To enable PHP in Apache add the following to httpd.conf and restart Apache:
LoadModule php5_module /usr/local/Cellar/php54/5.4.8/libexec/apache2/libphp5.so

Apache is not aware of the homebrew version of PHP (i.e. /usr/bin/php). You see it on the command line because you've likely modified your PATH (i.e. /usr/local/bin/php).

You can modify this in your httpd.conf file.

I am not a fan of homebrew or other package libraries. Primarily because Mac OS X is built atop Unix. Furthermore, all but MySQL are installed natively. Here's an article on installing Apache, MySQL, and PHP on Mac OS X.

Disclaimer: I wrote that article.